Difference between revisions of "Older News"

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= Older News=
 
= Older News=
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* PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
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* [[group]] command has been added.
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* The truly awesome [[grid_mode]] setting has been added.
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* [[Ellipsoids]] representation added for drawing thermal ellipsoids.
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* [[GetNamesInSel]] — find the names of all objects in a selection.
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* [[CalcArea]] — find the area of any given object/selection;
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* [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
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* [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
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* [[DrawBoundingBox]] — Draw a bounding box around your selection.
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* Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
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* Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
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* [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
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* [[LigAlign]] — Ligand-based active site alignment and comparison.
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* Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
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* Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests. ♦ New logo for the wiki.  It's DNA.  You can easily see the major/minor grooves.  If you don't see it, force a reload of the page (CTRL-F5, usually).
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* New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
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* [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
 
* [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!

Revision as of 04:56, 2 July 2009

Older News

  • PyMOL now comes with some builtin examples: look in the examples directory of your source tree.
  • group command has been added.
  • The truly awesome grid_mode setting has been added.
  • Ellipsoids representation added for drawing thermal ellipsoids.
  • GetNamesInSel — find the names of all objects in a selection.
  • CalcArea — find the area of any given object/selection;
  • ConnectedCloud — find connected clouds of objects in PyMOL.
  • MakeVinaCommand — Use PyMOL to create a valid command line for the new Vina docking software.
  • DrawBoundingBox — Draw a bounding box around your selection.
  • Locate loaded PyMOL objects that are nearby some other object with FindObjectsNearby.
  • Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with LoadDir.
  • PDB Web Services Script — Example using PyMOL and the PDB Web Services.
  • LigAlign — Ligand-based active site alignment and comparison.
  • Added a simple script for finding the center or mass, or moving a selection to the origin.
  • Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests. ♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
  • New category about PyMOL performance: making the impossible possible, and the difficult easier/faster.


  • ImmersiveViz -- Headtracking user interface for PyMOL (watch the video)!
  • Colorama --a PyMOL plugin which allows to color objects using adjustable scale bars
  • ProMOL plugin added. Catalytic site prediction, other tools. Redirects to website.
  • EMovie plugin added. Easy movies in PyMol using a GUI.
  • DYNMAP plugin page created. Check it out!
  • EZ-Viz
  • Stereo 3D Displays.
  • Massively restructured the TOPTOC and make the OLD_TOPTOC for the older version. Still need to add more content to the TOPTOC.
  • Added a simple script for removing specific alternately located atoms.
  • Added a starter gallery of PyMOL-created Journal Covers.
  • Added some information on how PyMOL handles Nonstandard_Amino_Acids.
  • Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been very fortunate to have hosting from BitGnome.Net; they've done an incredible job!
  • Gallery -- Did you make a cool image? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).
  • Updated the wiki. Also installed the newer GeSHI extension. Please keep an eye out for source code that is improperly tagged and so improperly formatted. See GeSHI Parameters.
  • Adding a special category/section for active PyMOL Development.
  • PyMOL 1.0 has been released!
  • PyMOL Official Documentation is also available for subscribers.





  • PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new
  1. Draw command and,
  2. Spheres Shader Spheres represenation
  • Also, Ray and Draw now show oversized images scaled into the viewport.
  • CE Align v0.8-RBS released. Better than before. See test case comparisons.
  • Slerpy, a set of pymol command extensions to simplify complex movie making is now available.
  • Updated the Kabsch code with a more elegant solution; fixed a small rotation bug.